The amount of greenhouse gases (GHG), especially, nitrous oxide (N2O) emitted from wastewater treatment plants (WWTP) using data reconciliation and closed-loop mass balance was estimated. This study is based on a flowbased emission estimation approach which depends on the accuracy of the measurement data. To reduce the (random) measurement error, data reconciliation was used to enhance the accuracy of the flow measurements. After performing data reconciliation, N2O emission was estimated with more precision by using the closed-loop mass balance. The results in both pilot-scale and full-scale plants show that the suggested method can easily obtain the precise flow measurement for GHG emission, which in turn, results in the accurate estimation of the N2O amounts emitted from WWTP. Moreover, it is shown that the estimated flowrate values can be used as a software sensor, which can replace the faulty sensors and can validate the existing field measurements.